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Background: I have been making a new website design at www.example.com/new which has been uploaded for some time as I have been redesigning the site. This site shares most of the same content as my current site at www.example.com.

Since I did not link to any of the pages on the new site, I thought Google would not index it, but it appears that it did. This would explain the fact that I have been experiencing a drop in SEO for my site.

Now that I have realized the problem, I will be replacing all the files in the /new directory with the duplicate files (i.e., replacing /new/gyms.html with /gyms.html) which should eliminate the duplicate content.

My question is, now that I will have fixed the problem of having duplicate content, will this SEO penalty go away? Will my rankings go back to the way they were? Will there always be some lingering effects?

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    You should be okay. It is penalty that effects placement in the SERPs and not actual rank. It will likely take a while to rebound though. Maybe a month or two to really see an upward trend again. Let this be an object lesson for everyone. If you put development code on your site, use the robots.txt file to block access. Assuming that Google will not find it regardless of the reason, is a mistake. Yes. The old days are gone where it was no big deal to develop within a directory with no links and expect it all to work. An ounce of caution saves much heart-ache.
    – closetnoc
    Commented Jul 14, 2014 at 0:37
  • Is there anything to accelerate the process? Will other positive SEO developments still boost my ranking?
    – etangins
    Commented Jul 14, 2014 at 0:52
  • As far as this penalty, no. I made a bad judgement call when redoing my titles, h1 tags, description tags. I took something out of the title tag and put it in the h1 tag. Simple huh? Bad idea. It has only been a couple of weeks and I am catching up to where I was a month before changing back. You will see a rebound as Google spiders your site again and realizes the difference. One idea to force Google to spider your site is to add a sitemap and add Google Search. Google will use the sitemap and spider your site quickly to enable the Google Search. Nice trick if you do not mind Google Search.
    – closetnoc
    Commented Jul 14, 2014 at 1:49
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    Another thought. I did not fully understand what you did to fix the problem, so forgive me if this is a bad idea. If you block the /new directory with your robots.txt file, the whole thing may go quicker without having to have Google re-spider the site. Anything in /new in the index will drop immediately and that will likely fix your problem the fastest.
    – closetnoc
    Commented Jul 14, 2014 at 1:55
  • by tonight, I am going to delete the /new directory and replace all of my current files on my site with the files on the /new directory (keep in mind the /new directory houses newer versions of each of the files on my site, but they have the same file name as the old files, so it's as easy as just replacing the file)
    – etangins
    Commented Jul 14, 2014 at 2:39

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The drop in visibility in search is almost certainly unrelated to the parallel website.

Almost all websites have content hosted on multiple URLs within the same website. That's something which search engines have to deal with. There's no reason to penalize a website for having that & certainly at Google there's no duplicate content penalty when it comes to your own content.

The effects you'd see (with content duplication within a website) are:

  • Google's algorithms will choose one URL to show for the content in search. Maybe it won't choose the URL you'd choose. If you have a preference, make it known (through redirects, rel=canonical, internal links, etc).

  • Depending on the amount of duplication (is each piece of content hosted 2x, 20x or 200x?), it can happen that the process of crawling is too much for the server, or that new/updated content isn't picked up as quickly as it otherwise might be.

With a "reasonable" amount of duplication (in your case, just 2x?) and with a reasonably strong server, neither of these are real problems. Most users won't notice the choice of URL, and crawling can still be sufficient.

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